Judging by initial physiological responses, rapidity of acquisition of drug-seeking or self-administration behavior, and strength of tendency to relapse, women and female laboratory animals are far more sensitive to cocaine than men and male laboratory animals. While it is well known that women differ from men in many emotional and cognitive responses, our understanding of the molecular underpinnings of these differences is limited. We will use deep sequencing to provide insight into the mechanisms that contribute to the different responses to withdrawal from cocaine observed in females and males. We previously applied this approach to the nucleus accumbens of male mice withdrawing from experimenter administered cocaine and identified the Wnt/cadherin pathway and miR-8 family members as key players. Targeted analysis of specific pathways revealed cocaine-mediated changes in the expression of mRNAs encoding multiple components of the dopamine, glutamate, GABA, acetylcholine, neuropeptide and endocannabinoid signaling pathways in the nucleus accumbens. In Aim 1, four groups of mice will be examined: males, cycling females, ovariectomized females and estradiol replaced ovariectomized females. Mice injected with saline or cocaine for a week will be sacrificed after four weeks of withdrawal; nucleus accumbens, prefrontal cortex and ventral tegmental area will be harvested for preparation of RNA. Duplicate bar-coded libraries prepared from the nucleus accumbens of mice exhibiting locomotor sensitization will be sequenced simultaneously, with technical replicates. Bioinformatic analysis will be used to identify cocaine-responsive transcripts and pathways common to all groups (core cocaine response), unique to females and sensitive to estrogen. In Aim 2 we will select transcripts and pathways from the core cocaine response group and female sensitivity group for validation and further analysis. The data set will allow analysis of the effets of sex, estrogen and cocaine on alternative splicing and RNA editing. Bioinformatic analysis of estrogen responsive elements and transcription factor binding sites in the promoter regions of cocaine-responsive genes will be undertaken. With this high quality, validated data set, focused sequencing studies can be used to analyze the response of individual mice self-administering cocaine. This broad approach should allow identification of therapeutic targets unique to females or sensitive to estrogen.